Protein Structure Lecture Notes PDF

Protein Structure  Protein Structure PH1123 Proteins are large molecules composed of several hundred amino acids. The linear sequence of amino acids in a peptide is referred to as the primary (1º) structure of the protein. A polypeptide chain is no...

Protein Structure  Protein Structure PH1123 Proteins are large molecules composed of several hundred amino acids. The linear sequence of amino acids in a peptide is referred to as the primary (1º) structure of the protein. A polypeptide chain is not linear and folds into a biologically active shape: The biologically active form is known as the native conformation The biological functions of many proteins can be explained on the basis of their conformations or shapes: Active site e.g. An enzyme folds to form an active site that can recognise substrate molecules:  Factors Effecting Protein Conformation: The Peptide Bond PH1123 The properties of the peptide bond has considerable impact on the shape and function of proteins. The peptide bond is planar, electron resonance gives 40 % double bond character. The peptide bond may be regarded as the average (below centre) of two extreme resonance forms. Some properties of the peptide bond are a result of its double bond character: The peptide bond is described as rigid & planar. Rotation around the peptide X bond not possible:  The Peptide Bond (2) PH1123 Peptide bonds have a trans conformation: Steric hindrance between side chain groups favours the trans conformation. Since the peptide bond is rigid, only two free movements exist in a polypeptide chain: Rotation about the C-N bond is called the phi () torsion angle. Rotation about the C -C bond is called the psi () torsion angle.   and  Bonds: Restricted Conformation PH1123 Protein conformation depends on  and  rotation. The flexibility of these bonds allows the primary sequence to fold into its native conformation Rotation is limited by: Steric hindrance - bulky groups e.g. side chains cannot approach each other. The rigidity of the peptide bond ultimately restricts movement. Favourable interactions (e.g. Hydrogen bonds) with other regions of the polypeptide chain (as we will see…….)  Secondary Structure: the -Helix PH1123 Secondary (2º) protein structure can be defined as ‘the three dimensional arrangement of the primary amino acid sequence’. The -helix is a secondary structure that results when consecutive amino acid residues have similar  and  torsion angle values:  = —57º,  = —47º The -helix is a SINGLE helix- don’t confuse with DNA 3.6 Amino acid residues are required for one complete turn of the helix Each backbone carbonyl oxygen is hydrogen bonded to the peptide nitrogen of the fourth residue along (towards C terminus), this is a favorable interaction that stabilizes the helix (Not all H bonds shown) Although hydrogen bonds are weak, they hold the helix structure together. Side chains (not shown above) are arranged on the outside of the helix.  Secondary Structure: the -Helix (2) PH1123 Glu Tyr Trp Trp Trp Val Trp Leu Helix peptide backbone highlighted with solid ribbon. Leu Side chains project outwards from the helix. Tyr  Secondary Structure: the -Helix (3) PH1123 Receptors are proteins rich in -helices. They usually contain a trans- membrane domain composed entirely of -helices. Crystal structure of the Adenosine Receptor (trans membrane domain) prevalent in cardiac tissue: Adenosine, a treatment for supraventricular tachycardia, binds to the trans- membrane domain.  Secondary structure:  Sheet PH1123 A  sheet is a secondary protein structure in which several strands (called  strands) of the peptide backbone are hydrogen bonded to themselves. The -sheet is an elongated, reasonably flat ‘sheet-like’ structure. Ala Val Inter-strand hydrogen bonds between backbone carbonyl oxygen and amide nitrogens stabilize the  sheet. In the  sheet, side chain interactions (mostly hydrophobic interactions between Hydrogen bond small groups) can provide additional Hydrophobic interaction stabilization.  Secondary structure:  Sheet (2) PH1123  Sheets come in two varieties...... Antiparallel  sheet Optimally hydrogen bonded, linear hydrogen bonds (better overlap = stronger bond), 2-15 strands possible (average 6) Parallel  sheet Hydrogen bonds distorted, sheet less stable, no more than 5 strands encountered.  Fibrous Proteins PH1123 Fibrous proteins contain only -helix secondary protein structure. They have a simple, elongated structure resembling threads or fibres. They provide mechanical support in skin, tendons and bones. They are physically durable, chemically inert and water insoluble. Structure maintained by hydrogen bonding within the -helix. Collagen from chicken cartilage: a triple coil of -helices  Fibrous Proteins: Hair PH1123 Hair is composed mostly of -keratin, a double coil of -helices. Many double coils are packed together to form a strand of hair. Protein structure is related to biological function. PH1123  Tertiary Protein Structure PH1123 Tertiary (3°) protein structure refers to the three dimensional (spatial) arrangement of secondary structure. Tertiary proteins, e.g. enzymes (left), usually contain an assortment of secondary features. Receptors (right) also have tertiary structure. The trans-membrane domain is usually attached to a cytoplasmic domain (i.e. a mixture of secondary structure) The precise structure of membrane bound receptors is extremely difficult to determine.  Globular Proteins PH1123 Globular proteins are tertiary proteins with greater structural diversity than fibrous proteins. All enzymes are globular proteins, every known structure is unique and complex. Some properties of globular proteins: Water soluble Compact, roughly spherical Tightly folded peptide chains Hydrophobic interior, hydrophilic surface Structure maintained by covalent and hydrogen bonding, non-covalent crosslinks and hydrophobic interactions. Possess indents or clefts - active site Enzymes - e.g. trypsin (both left) a protease enzyme. It is not as obvious how the tertiary structure of an enzyme is responsible for its properties……(see enzyme lectures)  Stabilization of Tertiary Structure: Hydrophobic Effect PH1123 Proteins are more stable in water (the body is mostly water!) with their hydrophobic side chains tucked into the protein interior. Non-polar substances will always minimize their contact with water. Non polar side chains aggregate, causing the protein to fold with non polar sidechains inside and polar sidechains outside the protein in contact with water. e.g. primary octapeptide: Folding Ser-Leu-Ala-Phe-Asp- Ala-Val-Thr (simplified backbone) Efficient packing maximizes van der Waals interactions between non polar residues and excludes water from the interior of the protein. Structure controls function: enzymes must be water soluble to function in cells! Val, Leu, Ile, Met, Phe and Ala are rarely encountered on protein exteriors  Stabilization of Tertiary Structure: Non-covalent Interactions PH1123 Proteins are arranged so virtually all possible hydrogen bonds are formed Polar side chains forced into Leu the protein interior can Val Asn neutralize their polarity by forming hydrogen bonds or Ser electrostatic interactions. Phe Asp Folding of a protein occurs to allow formation of all possible hydrogen bonds and hydrophobic interactions: Ala stabilize protein 3º structure Ala Lys Val  Stabilization of Tertiary Structure: Covalent Interactions PH1123 Disulfide bonds are covalent cross links that form between adjacent cysteine residues and help stabilize the conformations of some proteins: Met-Gly-Gln-Cys-Val-Asp-Phe-Ala Val-Lys-Asp-Cys-His-Tyr-Ala-Gly A covalent bond is very strong (compared to H bond or van der Waals) Disulfide links are especially common in proteins that are secreted from cells:  Effects of Temperature and pH on Tertiary Structure PH1123 In the laboratory, heating a chemical reaction usually increases the rate of the reaction. Enzymes however, function poorly at extremes of temperature or pH. Why? Heat / extreme pH Native (active) conformation Unfolded (inactive) Stabilizing Interactions conformation The tertiary structure of an enzyme is responsible for biological activity. Tertiary structure is maintained by weak interactions (mostly hydrogen bonds and van der Waals forces). Variations of pH or temperature disrupt the stabilising interactions, causing changes to the tertiary structure. The protein is said to be denatured. Enzymes have evolved to function (i.e. maximum stabilization of tertiary structure) at physiological conditions: pH 7.4 and 37 ºC.  Protein Structure: Quaternary Structure PH1123 Quaternary (4º) structure Refers to proteins that are composed of more than one polypeptide strand. Haemoglobin is composed of 4 globular protein subunits, two identical ‘ units’ containing 141 amino acids and two identical   ‘ units’ containing 146 amino acids. Each subunit contains an iron atom, vital for the transport of oxygen in the blood.   Insulin, a hormone that controls glucose metabolism consists of two peptide chains, linked and maintained in the biological active conformation by three disulfide bridges. Gly-Ile-Val-Glu-Gln-Cys-Cys-Ala-Ser-Val-Cys-Ser-Leu-Tyr-Gln-Leu-Glu-Asn-Tyr-Cys-Asn Phe-Val-Asn-Gln-His-Leu-Cys-Gly-Ser-His-Leu-Val-Glu-Ala-Leu-Tyr-Leu-Val-Cys-Gly-Glu-Arg-Gly-Phe-Phe-Tyr-Thr-Pro-Lys-Ala  Quaternary Structure: Haemoglobin PH1123  Coronavirus Spike Protein PH1123  Coronavirus Spike Protein: HR2 Domain PH1123  How are protein structures obtained? PH1123 “Photo 51” of DNA